Characterization of clinically used oral antiseptics as quadruplex-binding ligands

Nucleic Acids Res. 2018 Apr 6;46(6):2722-2732. doi: 10.1093/nar/gky084.


Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a widely used oral antiseptic, and the G-quadruplex (G4) structure in the KRAS oncogene promoter. The interaction of chlorhexidine and related drugs to the KRAS G4 is evaluated using multiple biophysical methods, including thermal melt, fluorescence titration and surface plasmon resonance (SPR) assays. Chlorhexidine has a specific low micromolar binding interaction with the G4, while related drugs have weaker and/or less specific interactions. Through NMR experiments and docking studies, we propose a plausible binding mode driven by both aromatic stacking and groove binding interactions. Additionally, cancer cell lines harbouring oncogenic mutations in the KRAS gene exhibit increased sensitivity to chlorhexidine. Treatment of breast cancer cells with chlorhexidine decreases KRAS protein levels, while a KRAS gene transiently expressed by a promoter lacking a G4 is not affected. This work confirms that known ligands bind broadly to G4 structures, while other drugs and druglike compounds can have more selective interactions that may be biologically relevant.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Anti-Infective Agents, Local / metabolism*
  • Anti-Infective Agents, Local / pharmacology
  • Binding Sites
  • Cell Line, Tumor
  • Cell Survival / drug effects
  • Chlorhexidine / metabolism*
  • Chlorhexidine / pharmacology
  • DNA / genetics
  • DNA / metabolism
  • G-Quadruplexes*
  • Gene Expression / drug effects
  • Humans
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Promoter Regions, Genetic / genetics
  • Proto-Oncogene Proteins p21(ras) / genetics
  • Proto-Oncogene Proteins p21(ras) / metabolism
  • Small Molecule Libraries / metabolism*
  • Small Molecule Libraries / pharmacology
  • Surface Plasmon Resonance


  • Anti-Infective Agents, Local
  • KRAS protein, human
  • Ligands
  • Small Molecule Libraries
  • DNA
  • Proto-Oncogene Proteins p21(ras)
  • Chlorhexidine